IRESite_Id:465 characteristics of UtrA IRES studied in pUTRA/CAT plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `465`	Version: `0`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vivo CMV driven transcript containing full length 5' UTR of mouse Utrn mRNA (from nt -506 to nt -1 of the
original sequence) cloned upstream of the beta-galactosidase.

The mRNA/+RNA sequence represented in the +DNA notation:

agagaaccca ctgcttactg gcttatcgaa attaatacga ctcactatag ggagacccaa gcttggtacc gagctcggat ccactagtaa cggccgccag 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgtgctggaa ttctgcagat atccatcaca ctggcggccg ctcgagttgt ggagtcgccc ttcccccgag gaggggagcg ggcagcgccg ggcgcgggat 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ttctcccgcc cagggccgag gaggagccct gggctcctca accgatcggg ccacctccgg gagcggcgcc ccttttcttt cgggtcattc ctgcagaggg 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

aaaactcctg cgtgcgcctg cccccaggct agcgtttgga ctgttttgtt tttggcggaa ctaccgggca ggaagattgc acaagtcagg gggcgtttcc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

aatcgggtgt caattttgga tctccccccc cccacccccc tttggatctt gtcgggcttt ccacgtttca cttaaaaaaa attcttgtaa cgtccaaggc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

aagctcccca cgacccgaac acgcccagag gaaccttggg gcctctgggg acttggctag caggtattca tgctagcctg gaccattttt cagatttagc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cttcagaaga ggatctggga aagcctttgg attatactga aactcattca agctcgagat ggagaaaaaa atcactggat ataccaccgt tgatatatcc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

caatggcatc gtaaagaaca ttttgaggca tttcagtcag ttgctcaatg tacctataac cagaccgttc agctggatat tacggccttt ttaaagaccg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

taaagaaaaa taagcacaag ttttatccgg cctttattca cattcttgcc cgcctgatga atgctcatcc ggaattccgt atggcaatga aagacggtga 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gctggtgata tgggatagtg ttcacccttg ttacaccgtt ttccatgagc aaactgaaac gttttcatcg ctctggagtg aataccacga cgatttccgg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cagtttctac acatatattc gcaagatgtg gcgtgttacg gtgaaaacct ggcctatttc cctaaagggt ttattgagaa tatgtttttc gtctcagcca 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

atccctgggt gagtttcacc agttttgatt taaacgtggc caatatggac aacttcttcg cccccgtttt caccatgggc aaatattata cgcaaggcga 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

caaggtgctg atgccgctgg cgattcaggt tcatcatgcc gtctgtgatg gcttccatgt cggcagaatg cttaatgaat tacaacagta ctgcgatgag 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tggcagggcg gggcgtaatt tttttaaggc agttattggt gcccttaaac gcctggtgct acgcctgaat aagtgataat aagcggatga atggcagaaa 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ttcgccggat ctttgtgaag gaaccttact tctgtggtgt gacataattg gacaaactac ctacagagat ttaaagctct aaggtaaata taaaattttt 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

aagtgtataa tgtgttaaac tactgattct aattgtttgt gtattttaga ttccaaccta tggaactgat gaatgggagc agtggtggaa tgcctttaat 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

gaggaaaacc tgttttgctc agaagaaatg ccatctagtg atgatgaggc tactgctgac tctcaacatt ctactcctcc aaaaaagaag agaaaggtag 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aagaccccaa ggactttcct tcagaattgc taagtttttt gagtcatgct gtgtttagta atagaactct tgcttgcttt gctatttaca ccacaaagga 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

aaaagctgca ctgctataca agaaaattat ggaaaaatat tctgtaacct ttataagtag gcataacagt tataatcata acatactgtt ttttcttact 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ccacacaggc atagagtgtc tgctattaat aactatgctc aaaaattgtg tacctttagc tttttaattt gtaaaggggt taataaggaa tatttgatgt 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

atagtgcctt gactagagat cataatcagc cataccacat ttgtagaggt tttacttgct ttaaaaaacc tcccacacct ccccctgaac ctgaaacata 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

aaatgaatgc aattgttgtt gttaacttgt ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

actgcattct agttgtggtt tgtccaaact catcaatgta tcttatcatg tctgcctaga gggccctatt ctatagtgtc acctaaatgc tagagctcgc 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

tgatcagcct cgactgtgcc ttctagttgc cagccatctg ttgtttgccc ctcccccgtg ccttccttga ccctggaagg tgccactccc actgtccttt 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

cctaataa
^2401

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pUTRA/CAT The name of the promoter used to express this mRNA:
CMV

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing full length 5' UTR of mouse Utrn mRNA (from nt -506 to nt -1 of the original sequence) and beta-galactosidase coding region.

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

not tested

A promoter reported in cDNA corresponding to IRES sequence:

no

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Mus musculus C2C12

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
Utrn

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Mus musculus C2C12

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

ggccgctcga gttgtggagt cgcccttccc ccgaggaggg gagcgggcag cgccgggcgc gggatttctc ccgcccaggg ccgaggagga gccctgggct 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cctcaaccga tcgggccacc tccgggagcg gcgccccttt tctttcgggt cattcctgca gagggaaaac tcctgcgtgc gcctgccccc aggctagcgt 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ttggactgtt ttgtttttgg cggaactacc gggcaggaag attgcacaag tcagggggcg tttccaatcg ggtgtcaatt ttggatctcc ccccccccac 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ccccctttgg atcttgtcgg gctttccacg tttcacttaa aaaaaattct tgtaacgtcc aaggcaagct ccccacgacc cgaacacgcc cagaggaacc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttggggcctc tggggacttg gctagcaggt attcatgcta gcctggacca tttttcagat ttagccttca gaagaggatc tgggaaagcc tttggattat 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

actgaaactc attcaagctc gagatggaga aaaaaatcac tggatatacc accgttgata tatcccaatg gcatcgtaaa gaacattttg aggcatttca 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

gtcagttgct caatgtacct ataaccagac cgttcagctg gatattacgg cctttttaaa gaccgtaaag aaaaataagc acaagtttta tccggccttt 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

attcacattc ttgcccgcct gatgaatgct catccggaat tccgtatggc aatgaaagac ggtgagctgg tgatatggga tagtgttcac ccttgttaca 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ccgttttcca tgagcaaact gaaacgtttt catcgctctg gagtgaatac cacgacgatt tccggcagtt tctacacata tattcgcaag atgtggcgtg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ttacggtgaa aacctggcct atttccctaa agggtttatt gagaatatgt ttttcgtctc agccaatccc tgggtgagtt tcaccagttt tgatttaaac 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gtggccaata tggacaactt cttcgccccc gttttcacca tgggcaaata ttatacgcaa ggcgacaagg tgctgatgcc gctggcgatt caggttcatc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

atgccgtctg tgatggcttc catgtcggca gaatgcttaa tgaattacaa cagtactgcg atgagtggca gggcggggcg taattttttt aaggcagtta 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ttggtgccct taaacgcctg gtgctacgcc tgaataagtg ataataagcg gatgaatggc agaaattcgc cggatctttg tgaaggaacc ttacttctgt 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ggtgtgacat aattggacaa actacctaca gagatttaaa gctctaaggt aaatataaaa tttttaagtg tataatgtgt taaactactg attctaattg 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tttgtgtatt ttagattcca acctatggaa ctgatgaatg ggagcagtgg tggaatgcct ttaatgagga aaacctgttt tgctcagaag aaatgccatc 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tagtgatgat gaggctactg ctgactctca acattctact cctccaaaaa agaagagaaa ggtagaagac cccaaggact ttccttcaga attgctaagt 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tttttgagtc atgctgtgtt tagtaataga actcttgctt gctttgctat ttacaccaca aaggaaaaag ctgcactgct atacaagaaa attatggaaa 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aatattctgt aacctttata agtaggcata acagttataa tcataacata ctgttttttc ttactccaca caggcataga gtgtctgcta ttaataacta 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tgctcaaaaa ttgtgtacct ttagcttttt aatttgtaaa ggggttaata aggaatattt gatgtatagt gccttgacta gagatcataa tcagccatac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cacatttgta gaggttttac ttgctttaaa aaacctccca cacctccccc tgaacctgaa acataaaatg aatgcaattg ttgttgttaa cttgtttatt 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gcagcttata atggttacaa ataaagcaat agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc aaactcatca 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

atgtatctta tcatgtctgc ctagagggcc ctattctata gtgtcaccta aatgctagag ctcgctgatc agcctcgact gtgccttcta gttgccagcc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

atctgttgtt tgcccctccc ccgtgccttc cttgaccctg gaaggtgcca ctcccactgt cctttcctaa taaaatgagg aaattgcatc gcattgtctg 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

agtaggtgtc attctattct ggggggtggg gtggggcagg acagcaaggg ggaggattgg gaagacaata gcaggcatgc tggggatgcg gtgggctcta 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tggcttctga ggcggaaaga accagctggg gctctagggg gtatccccac gcgccctgta gcggcgcatt aagcgcggcg ggtgtggtgg ttacgcgcag 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

cgtgaccgct acacttgcca gcgccctagc gcccgctcct ttcgctttct tcccttcctt tctcgccacg ttcgccggct ttccccgtca agctctaaat 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

cggggcatcc ctttagggtt ccgatttagt gctttacggc acctcgaccc caaaaaactt gattagggtg atggttcacg tagtgggcca tcgccctgat 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

agacggtttt tcgccctttg acgttggagt ccacgttctt taatagtgga ctcttgttcc aaactggaac aacactcaac cctatctcgg tctattcttt 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

tgatttataa gggattttgg ggatttcggc ctattggtta aaaaatgagc tgatttaaca aaaatttaac gcgaattaat tctgtggaat gtgtgtcagt 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tagggtgtgg aaagtcccca ggctccccag gcaggcagaa gtatgcaaag catgcatctc aattagtcag caaccaggtg tggaaagtcc ccaggctccc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccata gtcccgcccc taactccgcc catcccgccc ctaactccgc ccagttccgc 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ccattctccg ccccatggct gactaatttt ttttatttat gcagaggccg aggccgcctc tgcctctgag ctattccaga agtagtgagg aggctttttt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ggaggcctag gcttttgcaa aaagctcccg ggagcttgta tatccatttt cggatctgat caagagacag gatgaggatc gtttcgcatg attgaacaag 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

atggattgca cgcaggttct ccggccgctt gggtggagag gctattcggc tatgactggg cacaacagac aatcggctgc tctgatgccg ccgtgttccg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

gctgtcagcg caggggcgcc cggttctttt tgtcaagacc gacctgtccg gtgccctgaa tgaactgcag gacgaggcag cgcggctatc gtggctggcc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

acgacgggcg ttccttgcgc agctgtgctc gacgttgtca ctgaagcggg aagggactgg ctgctattgg gcgaagtgcc ggggcaggat ctcctgtcat 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ctcaccttgc tcctgccgag aaagtatcca tcatggctga tgcaatgcgg cggctgcata cgcttgatcc ggctacctgc ccattcgacc accaagcgaa 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

acatcgcatc gagcgagcac gtactcggat ggaagccggt cttgtcgatc aggatgatct ggacgaagag catcaggggc tcgcgccagc cgaactgttc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

gccaggctca aggcgcgcat gcccgacggc gaggatctcg tcgtgaccca tggcgatgcc tgcttgccga atatcatggt ggaaaatggc cgcttttctg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gattcatcga ctgtggccgg ctgggtgtgg cggaccgcta tcaggacata gcgttggcta cccgtgatat tgctgaagag cttggcggcg aatgggctga 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ccgcttcctc gtgctttacg gtatcgccgc tcccgattcg cagcgcatcg ccttctatcg ccttcttgac gagttcttct gagcgggact ctggggttcg 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

aaatgaccga ccaagcgacg cccaacctgc catcacgaga tttcgattcc accgccgcct tctatgaaag gttgggcttc ggaatcgttt tccgggacgc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

cggctggatg atcctccagc gcggggatct catgctggag ttcttcgccc accccaactt gtttattgca gcttataatg gttacaaata aagcaatagc 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

atcacaaatt tcacaaataa agcatttttt tcactgcatt ctagttgtgg tttgtccaaa ctcatcaatg tatcttatca tgtctgtata ccgtcgacct 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ctagctagag cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc tcacaattcc acacaacata cgagccggaa gcataaagtg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

taaagcctgg ggtgcctaat gagtgagcta actcacatta attgcgttgc gctcactgcc cgctttccag tcgggaaacc tgtcgtgcca gctgcattaa 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

tgaatcggcc aacgcgcggg gagaggcggt ttgcgtattg ggcgctcttc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag gaaagaacat gtgagcaaaa ggccagcaaa aggccaggaa 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ccgtaaaaag gccgcgttgc tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cgggaagcgt ggcgctttct caatgctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag ccactggtaa caggattagc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

agagcgaggt atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa ctacggctac actagaagga cagtatttgg tatctgcgct ctgctgaagc 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

aaaaaaagga tctcaagaag atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga ttttggtcat gagattatca 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

aaaaggatct tcacctagat ccttttaaat taaaaatgaa gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta gataactacg atacgggagg gcttaccatc 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

tggccccagt gctgcaatga taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa gggccgagcg cagaagtggt 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag gcgagttaca tgatccccca tgttgtgcaa 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

aaaagcggtt agctccttcg gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag cactgcataa ttctcttact 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg gcgaaaactc tcaaggatct taccgctgtt 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

gagatccagt tcgatgtaac ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag caaaaacagg aaggcaaaat 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt gccacctgac gtcgacggat cgggagatct 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

cccgatcccc tatggtcgac tctcagtaca atctgctctg atgccgcata gttaagccag tatctgctcc ctgcttgtgt gttggaggtc gctgagtagt 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

gcgcgagcaa aatttaagct acaacaaggc aaggcttgac cgacaattgc atgaagaatc tgcttagggt taggcgtttt gcgctgcttc gcgatgtacg 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ggccagatat acgcgttgac attgattatt gactagttat taatagtaat caattacggg gtcattagtt catagcccat atatggagtt ccgcgttaca 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

taacttacgg taaatggccc gcctggctga ccgcccaacg acccccgccc attgacgtca ataatgacgt atgttcccat agtaacgcca atagggactt 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

tccattgacg tcaatgggtg gactatttac ggtaaactgc ccacttggca gtacatcaag tgtatcatat gccaagtacg ccccctattg acgtcaatga 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

cggtaaatgg cccgcctggc attatgccca gtacatgacc ttatgggact ttcctacttg gcagtacatc tacgtattag tcatcgctat taccatggtg 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

atgcggtttt ggcagtacat caatgggcgt ggatagcggt ttgactcacg gggatttcca agtctccacc ccattgacgt caatgggagt ttgttttggc 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

accaaaatca acgggacttt ccaaaatgtc gtaacaactc cgccccattg acgcaaatgg gcggtaggcg tgtacggtgg gaggtctata taagcagagc 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

tctctggcta actagagaac ccactgctta ctggcttatc gaaattaata cgactcacta tagggagacc caagcttggt accgagctcg gatccactag 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

taacggccgc cagtgtgctg gaattctgca gatatccatc acactggc
^7501      ^7511      ^7521      ^7531      ^7541

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

1

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyl transferase

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

The ORF absolute position (the base range includes START and STOP codons or their equivalents):

659-1318

Remarks:

The plasmid was used as the control for experiments in article The Utrophin A 5'-Untranslated Region Confers
Internal Ribosome Entry Site-mediated Translational Control during Regeneration of Skeletal Muscle Fibers
(Miura et al., 2005; PMID:16061482).

Citations:

Miura P., Thompson J., Chakkalakal J. V., Holcik M., Jasmin B. J. (2005) The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J. Biol. Chem. 280(38):32997-33005

IRESs:

IRES:

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `UtrA`	The functional status of IRES: `functional`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

147-652

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

ttgtggagtc gcccttcccc cgaggagggg agcgggcagc gccgggcgcg ggatttctcc cgcccagggc cgaggaggag ccctgggctc ctcaaccgat 
^147       ^157       ^167       ^177       ^187       ^197       ^207       ^217       ^227       ^237       

cgggccacct ccgggagcgg cgcccctttt ctttcgggtc attcctgcag agggaaaact cctgcgtgcg cctgccccca ggctagcgtt tggactgttt 
^247       ^257       ^267       ^277       ^287       ^297       ^307       ^317       ^327       ^337       

tgtttttggc ggaactaccg ggcaggaaga ttgcacaagt cagggggcgt ttccaatcgg gtgtcaattt tggatctccc cccccccacc cccctttgga 
^347       ^357       ^367       ^377       ^387       ^397       ^407       ^417       ^427       ^437       

tcttgtcggg ctttccacgt ttcacttaaa aaaaattctt gtaacgtcca aggcaagctc cccacgaccc gaacacgccc agaggaacct tggggcctct 
^447       ^457       ^467       ^477       ^487       ^497       ^507       ^517       ^527       ^537       

ggggacttgg ctagcaggta ttcatgctag cctggaccat ttttcagatt tagccttcag aagaggatct gggaaagcct ttggattata ctgaaactca 
^547       ^557       ^567       ^577       ^587       ^597       ^607       ^617       ^627       ^637       

ttcaag
^647

Remarks:

Whole 5'-UTR region of Utrn mRNA (from nt -506 to nt -1 of the original sequence).

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1